In order to insert a sequence element (a tag sequence) into an existing nucleic acid, in particular at the 3′ end, it was necessary, until now, to carry out a nucleic acid synthesis of the opposite strand of the developing nucleic acid or the ligation of a so-called adaptor/linker. These well known methods are time consuming and laborious. At present, three different methods are known for inserting specific tag sequences at the 3′ ends of nucleic acids that are comprised of the common steps that (a) an opposite strand is produced for nucleic acid already synthesized in a polymerase reaction or (b) a second enzymatic reaction is needed in order to attach a tag sequence to a nucleic acid. The following three methods are concerned:
1) Earlier, a template-independent DNA polymerase was used to attach a homopolymer at the 3′ end of DNA. A template-independent polymerase, which polymerizes the homopolymer in an independent reaction, is necessary according to this method. This method can thus be extended in that an oligonucleotide containing a sequence, which is complementary to the attached homopolymer, can specifically activate the synthesis of the opposite strand. This method was originally used with cDNA cloning (Okayama H. & Berg P., High-Efficiency Cloning of Full-Length cDNA, Mol. Cell. Biol. 1982, 161-170). Nowadays, this method is also used for RNA linear amplification.
2) Furthermore, it is also known to use a so-called “template-switching primer” that inserts a specific tag sequence at the mRNA cap end (Matz M., Shagin D., Bogdanova E., Britanova O., Lukyanov S., Diatchenko L. & Chenchik A., Amplification of cDNA ends based on template-switching effect and step-out PCR, Nucl. Acid Res., 1999, Vol. 27, No. 6, 1558-1560; U.S. Pat. No. 5,962,272). This method is directly linked to the property of a certain reverse transcriptase, Rnase H-MMLV, in order to attach cytosine nucleotides template-independently at the RNA cap end. This attachment of nucleotides corresponds to a polymer tailing already described under 1), however carried out here with the reverse transcriptase. The cytosine nucleotides can be used for hybridizing an oligonucleotide having G bases at the 3′ end. This method is used in cDNA cloning for example.
3) Finally, the opposite strand can also be activated with a primer which is attached externally. This oligonucleotide primer, for example, can contain a specific sequence (tag sequence) at its 5′ end in addition to a random sequence, whereby a tag sequence is inserted at the 5′ end in the newly synthesized strand. This form of synthesis utilizes a primer with a tag sequence; however, the synthesis of the opposite strand is necessary in each case in order to insert a complementary sequence to the tag sequence at the 3′ end. This method is used, for example, in cDNA cloning or amplification reactions.
Thus, for example, US patent application no. 2003/0143599 by Makarov et al. describes a method for producing a DNA molecule that is subsequently cut into random fragments. Then, a primer with an essentially well known sequence is attached to at least one of the fragments produced in order to produce “primer-linked fragments,” which are then amplified. However, in the method according to the aforementioned US patent application, the primer is inserted at the 3′ end of the resulting DNA fragment by a so-called “tailing” or an adaptor ligation.
Finally, an article (Wharam S. D., Marsh P., Lloyd J. S., Ray T. D., Mock G. A., Assenberg R., McPhee J. E., Brown P., Weston A. and Cardy D. L. N., Specific detection of DNA and RNA targets using a novel isothermal nucleic acid amplification assay based on the formation of a three-way junction structure, Nucleic Acids Research, 2001, Vol. 29, No. 11 e54, 1-8) describes the detection of certain DNA or RNA sequences using oligonucleotides with which, however, no “template switch” takes place. Instead, in this case, an oligonucleotide (called an “extension probe”) is extended, which binds both to the target sequence, as well as to the “template probe,” so that a y- or t-shaped “three-way junction” is formed.
The problem addressed by the present invention is to provide a new method for inserting sequence elements (tag sequences) into nucleic acids which avoids the complexity of the well known multi-step methods described above and which inserts a tag sequence into a first polymerase reaction without subsequent synthesis of the opposite strand at the 3′ end of the newly synthesized nucleic acid. The solution to this problem is a method for inserting a tag sequence or several tag sequences into a nucleic acid and is characterized by the following steps:                (a) provision of a template nucleic acid;        (b) hybridization of at least one anchor sequence of at least one anchor oligonucleotide with at least one sequence fragment of the template nucleic acid and        (c) synthesis of a new strand of nucleic acid, which partially complements the template nucleic acid and which contains a sequence complimentary to the non-hybridized portion of the anchor oligonucleotide i.e. at least one template tag sequence, at its 3′ end, whereby a double-stranded region of nucleic acid is formed.        
Additional advantageous embodiments, aspects and details of the method according to the invention are found in the patent claims, description, and examples, as well as the figures.